The Cytotoxic Cell Studies Group has made significant advances in our study of the murine Ly49 gene family. Our laboratory has identified eight novel Ly49 genes in the 129/J mouse strain. We have constructed a bacterial artificial chromosome (BAC) contig map of the 129/J Ly49 gene cluster, and it demonstrates significant differences in the gene number and organization as compared to B6 mice. The number and type of human killer cell inhibitory receptor (KIR) genes is also highly variable, therefore this finding establishes another parallel between the murine Ly49s and the human KIR family of class I MHC receptors and reinforces the study of the Ly49 system as a model for human KIR function. We have investigated the MHC class I specificity of the novel Ly49 receptors and shown that Ly49 alleles can possess very different patterns of class I MHC recognition. Our studies of the Ly49 promoter structure have led to the identification of an additional upstream promoter that is active early in NK cell differentiation. We have characterized the early promoters of several Ly49 genes and the importance of the early promoter in selective Ly49 gene activation is currently under investigation.